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Molecular Evolution of Regulatory Genes in Spruces from Different Species and Continents: Heterogeneous Patterns of Linkage Disequilibrium and Selection but Correlated Recent Demographic Changes

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Molecular Evolution of Regulatory Genes in Spruces from Different Species and Continents: Heterogeneous Patterns of Linkage Disequilibrium and Selection but Correlated Recent Demographic Changes

Content Provider	Springer Nature Link
Author	Namroud, Marie Claire Guillet Claude, Carine Mackay, John Isabel, Nathalie Bousquet, Jean
Copyright Year	2010
Abstract	Genes involved in transcription regulation may represent valuable targets in association genetics studies because of their key roles in plant development and potential selection at the molecular level. Selection and demographic signatures at the sequence level were investigated for five regulatory genes belonging to the knox-I family (KN1, KN2, KN3, KN4) and the HD-Zip III family (HB-3) in three Picea species affected by post-glacial recolonization in North America and Europe. To disentangle neutral and selective forces and estimate linkage disequilibrium (LD) on a gene basis, complete or nearly complete gene sequences were analysed. Nucleotide variation within species, haplotype structure, LD, and neutrality tests, in addition to coalescent simulations based on Tajima’s D and Fay and Wu’s H, were estimated. Nucleotide diversity was generally low in all species (average π = 0.002–0.003) and much heterogeneity was seen in LD and selection signatures among genes and species. Most of the genes harboured an excess of both rare and frequent alleles in the three species. Simulations showed that this excess was significantly higher than that expected under neutrality and a bottleneck during the Last Glacial Maximum followed by population expansion at the Pleistocene/Holocene boundary or shortly after best explains the correlated sequence patterns. These results indicate that despite recent large demographic changes in the three boreal species from two continents, species-specific selection signatures could still be detected from the analysis of nearly complete regulatory gene sequences. Such different signatures indicate differential subfunctionalization of gene family members in the three congeneric species.
Starting Page	371
Ending Page	386
Page Count	16
File Format	PDF
ISSN	00222844
Journal	Journal of Molecular Evolution
Volume Number	70
Issue Number	4
e-ISSN	14321432
Language	English
Publisher	Springer-Verlag
Publisher Date	2010-03-31
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Bottleneck HD-Zip III knox-I Linkage disequilibrium Picea Population expansion Selection signatures Animal Genetics and Genomics Plant Genetics & Genomics Plant Sciences Microbiology Evolutionary Biology Cell Biology
Content Type	Text
Resource Type	Article
Subject	Genetics Molecular Biology Ecology, Evolution, Behavior and Systematics

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Molecular Evolution of Regulatory Genes in Spruces from Different Species and Continents: Heterogeneous Patterns of Linkage Disequilibrium and Selection but Correlated Recent Demographic Changes

Bousquet J: Molecular evolution of regulatory genes in spruces from different species and continents: heterogeneous patterns of linkage disequilibrium and selection but correlated recent demographic changes

Molecular Evolution of Regulatory Genes in Spruces from Different Species and Continents: Heterogeneous Patterns of Linkage Disequilibrium and Selection but Correlated Recent Demographic Changes

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Molecular Evolution of Regulatory Genes in Spruces from Different Species and Continents: Heterogeneous Patterns of Linkage Disequilibrium and Selection but Correlated Recent Demographic Changes

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Molecular Evolution of Regulatory Genes in Spruces from Different Species and Continents: Heterogeneous Patterns of Linkage Disequilibrium and Selection but Correlated Recent Demographic Changes

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Molecular Evolution of Regulatory Genes in Spruces from Different Species and Continents: Heterogeneous Patterns of Linkage Disequilibrium and Selection but Correlated Recent Demographic Changes